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Detailed information for vg0623386254:

Variant ID: vg0623386254 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 23386254
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


TCATTCTTTCCTAGAGAAACCCCTAATTTAGAAAAATTTGCAGCAAGAGTCTTATCTGGAATTGAAGCAACAGAATTTGTGGTATTAAACTTGTTACCTG[T/C]
TAGCGTCTCGAGGTTATGAACCTTTTTAAGCAGCTCTGCCCGGTTTGCCACCGGCGCATCTGCATTTGCCATCGCCTTCTGTCTTTCACTTTGCCTAGTT

Reverse complement sequence

AACTAGGCAAAGTGAAAGACAGAAGGCGATGGCAAATGCAGATGCGCCGGTGGCAAACCGGGCAGAGCTGCTTAAAAAGGTTCATAACCTCGAGACGCTA[A/G]
CAGGTAACAAGTTTAATACCACAAATTCTGTTGCTTCAATTCCAGATAAGACTCTTGCTGCAAATTTTTCTAAATTAGGGGTTTCTCTAGGAAAGAATGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 38.20% 6.50% 5.63% 49.75% NA
All Indica  2759 45.90% 11.00% 6.34% 36.72% NA
All Japonica  1512 21.10% 0.00% 0.99% 77.91% NA
Aus  269 58.70% 0.00% 25.28% 15.99% NA
Indica I  595 49.60% 9.90% 9.75% 30.76% NA
Indica II  465 32.90% 11.40% 2.80% 52.90% NA
Indica III  913 52.70% 11.80% 5.81% 29.68% NA
Indica Intermediate  786 43.00% 10.70% 6.49% 39.82% NA
Temperate Japonica  767 34.20% 0.00% 1.17% 64.67% NA
Tropical Japonica  504 6.20% 0.00% 0.99% 92.86% NA
Japonica Intermediate  241 10.80% 0.00% 0.41% 88.80% NA
VI/Aromatic  96 27.10% 0.00% 4.17% 68.75% NA
Intermediate  90 36.70% 2.20% 4.44% 56.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0623386254 T -> C LOC_Os06g39400.1 missense_variant ; p.Thr684Ala; MODERATE nonsynonymous_codon ; T684A Average:58.043; most accessible tissue: Minghui63 root, score: 71.702 unknown unknown TOLERATED 0.85
vg0623386254 T -> DEL LOC_Os06g39400.1 N frameshift_variant Average:58.043; most accessible tissue: Minghui63 root, score: 71.702 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0623386254 NA 3.09E-06 mr1547 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0623386254 1.08E-09 6.69E-12 mr1709 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0623386254 1.14E-08 3.20E-10 mr1709 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0623386254 NA 9.76E-07 mr1547_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0623386254 NA 3.27E-08 mr1547_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0623386254 5.43E-14 9.24E-12 mr1709_2 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0623386254 3.60E-10 1.54E-10 mr1709_2 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251